Literature DB >> 14681466

Human protein reference database as a discovery resource for proteomics.

Suraj Peri1, J Daniel Navarro, Troels Z Kristiansen, Ramars Amanchy, Vineeth Surendranath, Babylakshmi Muthusamy, T K B Gandhi, K N Chandrika, Nandan Deshpande, Shubha Suresh, B P Rashmi, K Shanker, N Padma, Vidya Niranjan, H C Harsha, Naveen Talreja, B M Vrushabendra, M A Ramya, A J Yatish, Mary Joy, H N Shivashankar, M P Kavitha, Minal Menezes, Dipanwita Roy Choudhury, Neelanjana Ghosh, R Saravana, Sreenath Chandran, Sujatha Mohan, Chandra Kiran Jonnalagadda, C K Prasad, Chandan Kumar-Sinha, Krishna S Deshpande, Akhilesh Pandey.   

Abstract

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.

Entities:  

Mesh:

Substances:

Year:  2004        PMID: 14681466      PMCID: PMC308804          DOI: 10.1093/nar/gkh070

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  17 in total

1.  RefSeq and LocusLink: NCBI gene-centered resources.

Authors:  K D Pruitt; D R Maglott
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

Review 2.  Towards an understanding of complex protein networks.

Authors:  C L Tucker; J F Gera; P Uetz
Journal:  Trends Cell Biol       Date:  2001-03       Impact factor: 20.808

3.  Initial sequencing and analysis of the human genome.

Authors:  E S Lander; L M Linton; B Birren; C Nusbaum; M C Zody; J Baldwin; K Devon; K Dewar; M Doyle; W FitzHugh; R Funke; D Gage; K Harris; A Heaford; J Howland; L Kann; J Lehoczky; R LeVine; P McEwan; K McKernan; J Meldrim; J P Mesirov; C Miranda; W Morris; J Naylor; C Raymond; M Rosetti; R Santos; A Sheridan; C Sougnez; Y Stange-Thomann; N Stojanovic; A Subramanian; D Wyman; J Rogers; J Sulston; R Ainscough; S Beck; D Bentley; J Burton; C Clee; N Carter; A Coulson; R Deadman; P Deloukas; A Dunham; I Dunham; R Durbin; L French; D Grafham; S Gregory; T Hubbard; S Humphray; A Hunt; M Jones; C Lloyd; A McMurray; L Matthews; S Mercer; S Milne; J C Mullikin; A Mungall; R Plumb; M Ross; R Shownkeen; S Sims; R H Waterston; R K Wilson; L W Hillier; J D McPherson; M A Marra; E R Mardis; L A Fulton; A T Chinwalla; K H Pepin; W R Gish; S L Chissoe; M C Wendl; K D Delehaunty; T L Miner; A Delehaunty; J B Kramer; L L Cook; R S Fulton; D L Johnson; P J Minx; S W Clifton; T Hawkins; E Branscomb; P Predki; P Richardson; S Wenning; T Slezak; N Doggett; J F Cheng; A Olsen; S Lucas; C Elkin; E Uberbacher; M Frazier; R A Gibbs; D M Muzny; S E Scherer; J B Bouck; E J Sodergren; K C Worley; C M Rives; J H Gorrell; M L Metzker; S L Naylor; R S Kucherlapati; D L Nelson; G M Weinstock; Y Sakaki; A Fujiyama; M Hattori; T Yada; A Toyoda; T Itoh; C Kawagoe; H Watanabe; Y Totoki; T Taylor; J Weissenbach; R Heilig; W Saurin; F Artiguenave; P Brottier; T Bruls; E Pelletier; C Robert; P Wincker; D R Smith; L Doucette-Stamm; M Rubenfield; K Weinstock; H M Lee; J Dubois; A Rosenthal; M Platzer; G Nyakatura; S Taudien; A Rump; H Yang; J Yu; J Wang; G Huang; J Gu; L Hood; L Rowen; A Madan; S Qin; R W Davis; N A Federspiel; A P Abola; M J Proctor; R M Myers; J Schmutz; M Dickson; J Grimwood; D R Cox; M V Olson; R Kaul; C Raymond; N Shimizu; K Kawasaki; S Minoshima; G A Evans; M Athanasiou; R Schultz; B A Roe; F Chen; H Pan; J Ramser; H Lehrach; R Reinhardt; W R McCombie; M de la Bastide; N Dedhia; H Blöcker; K Hornischer; G Nordsiek; R Agarwala; L Aravind; J A Bailey; A Bateman; S Batzoglou; E Birney; P Bork; D G Brown; C B Burge; L Cerutti; H C Chen; D Church; M Clamp; R R Copley; T Doerks; S R Eddy; E E Eichler; T S Furey; J Galagan; J G Gilbert; C Harmon; Y Hayashizaki; D Haussler; H Hermjakob; K Hokamp; W Jang; L S Johnson; T A Jones; S Kasif; A Kaspryzk; S Kennedy; W J Kent; P Kitts; E V Koonin; I Korf; D Kulp; D Lancet; T M Lowe; A McLysaght; T Mikkelsen; J V Moran; N Mulder; V J Pollara; C P Ponting; G Schuler; J Schultz; G Slater; A F Smit; E Stupka; J Szustakowki; D Thierry-Mieg; J Thierry-Mieg; L Wagner; J Wallis; R Wheeler; A Williams; Y I Wolf; K H Wolfe; S P Yang; R F Yeh; F Collins; M S Guyer; J Peterson; A Felsenfeld; K A Wetterstrand; A Patrinos; M J Morgan; P de Jong; J J Catanese; K Osoegawa; H Shizuya; S Choi; Y J Chen; J Szustakowki
Journal:  Nature       Date:  2001-02-15       Impact factor: 49.962

4.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

5.  Integrated genomic and proteomic analyses of a systematically perturbed metabolic network.

Authors:  T Ideker; V Thorsson; J A Ranish; R Christmas; J Buhler; J K Eng; R Bumgarner; D R Goodlett; R Aebersold; L Hood
Journal:  Science       Date:  2001-05-04       Impact factor: 47.728

6.  Guidelines for human gene nomenclature.

Authors:  Hester M Wain; Elspeth A Bruford; Ruth C Lovering; Michael J Lush; Mathew W Wright; Sue Povey
Journal:  Genomics       Date:  2002-04       Impact factor: 5.736

Review 7.  Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases.

Authors:  M Mann; A Pandey
Journal:  Trends Biochem Sci       Date:  2001-01       Impact factor: 13.807

8.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders.

Authors:  Ada Hamosh; Alan F Scott; Joanna Amberger; Carol Bocchini; David Valle; Victor A McKusick
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

9.  The Pfam protein families database.

Authors:  Alex Bateman; Ewan Birney; Lorenzo Cerruti; Richard Durbin; Laurence Etwiller; Sean R Eddy; Sam Griffiths-Jones; Kevin L Howe; Mhairi Marshall; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

10.  The sequence of the human genome.

Authors:  J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; H O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; J R Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G Subramanian; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; A G Clark; J Nadeau; V A McKusick; N Zinder; A J Levine; R J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; S Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; S Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; D Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; E Suh; R Thomas; N N Tint; S Tse; C Vech; G Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; J F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Deslattes Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
Journal:  Science       Date:  2001-02-16       Impact factor: 47.728

View more
  255 in total

1.  Human protein reference database and human proteinpedia as discovery resources for molecular biotechnology.

Authors:  Renu Goel; Babylakshmi Muthusamy; Akhilesh Pandey; T S Keshava Prasad
Journal:  Mol Biotechnol       Date:  2011-05       Impact factor: 2.695

2.  The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study.

Authors:  Roberto Romero; Offer Erez; Eli Maymon; Piya Chaemsaithong; Zhonghui Xu; Percy Pacora; Tinnakorn Chaiworapongsa; Bogdan Done; Sonia S Hassan; Adi L Tarca
Journal:  Am J Obstet Gynecol       Date:  2017-03-03       Impact factor: 8.661

3.  Predicting subcellular localization via protein motif co-occurrence.

Authors:  Michelle S Scott; David Y Thomas; Michael T Hallett
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

4.  Topological network alignment uncovers biological function and phylogeny.

Authors:  Oleksii Kuchaiev; Tijana Milenkovic; Vesna Memisevic; Wayne Hayes; Natasa Przulj
Journal:  J R Soc Interface       Date:  2010-03-17       Impact factor: 4.118

5.  Large-scale phosphorylation analysis of mouse liver.

Authors:  Judit Villén; Sean A Beausoleil; Scott A Gerber; Steven P Gygi
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-22       Impact factor: 11.205

6.  Modelling protein-protein interaction networks via a stickiness index.

Authors:  Natasa Przulj; Desmond J Higham
Journal:  J R Soc Interface       Date:  2006-10-22       Impact factor: 4.118

7.  Quantitative systems-level determinants of human genes targeted by successful drugs.

Authors:  Lixia Yao; Andrey Rzhetsky
Journal:  Genome Res       Date:  2007-12-14       Impact factor: 9.043

8.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

9.  RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins.

Authors:  Noel G Faux; Gavin A Huttley; Khalid Mahmood; Geoffrey I Webb; Maria Garcia de la Banda; James C Whisstock
Journal:  Genome Res       Date:  2007-06-13       Impact factor: 9.043

10.  Module cover - a new approach to genotype-phenotype studies.

Authors:  Yoo-Ah Kim; Raheleh Salari; Stefan Wuchty; Teresa M Przytycka
Journal:  Pac Symp Biocomput       Date:  2013
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.